2014-09-21 8:53 GMT-06:00 Sikandar Mashayak <[email protected]>:
> Hi,
>
> I am trying to set up a coarse-graining simulation with LAMMPS as a
> simulation program. However, I am not quite sure how to specify the mapping
> and topology info. In the spce/ibi_lammps example, there is a topol.xml file
> for CG topology, but its structure is not clear to me, especially terms like
> topology base and first. Also, can anyone give me an example of mapping
> using LAMMPS trajectory files?
topol.xml looks like:
<topology base="spce.dump">
<molecules>
<clear/>
<define name="SOL" first="1" nbeads="1" nmols="2180"/>
</molecules>
</topology>
The base="spce.dump" means read "spce.dump" and setup topology
information like given therein.
In the case of a dump file, VOTCA reads the atom types (an integer,
hence type1="1" in settings.xml), positions and the box size, all in
lammps units.
For other file formats like gro, xyz or pdb as base, things might be
different as some of them don't have box sizes.
The dump file contains no information about which atoms belong to
which molecule.
For that
<clear/>
<define name="SOL" first="1" nbeads="1" nmols="2180"/>
is used. <clear/> removed all molecule read (in case of a dump file
none), but it don't hurt to do it.
Then we setup 2180(=nmols) molecules with 1(=nbeads) bead each
starting from atom "1"(=first).
That is it. For more complicated system you can have multiple of these lines.
You don't need to use a dump file as a topology base, a pdb will do, too.
But for a pdb you will need to set the box using a line like
<box xx="4.03100" yy="4.03100" zz="4.03100"/>
inside the <topology> block.
Christoph
>
> Thanks,
> Sikandar
>
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--
Christoph Junghans
Web: http://www.compphys.de
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